I don't find putting Cullen back on lyrium irrational at all. In fact, I think it's the sensible, pragmatic thing to do if you care about how your organisation performs under his command. (Not that rational, pragmatic and sensible is always the right thing to do, either. But anyway.) He should be in his top form if he is to lead our forces. It's one of the decisions where I fully realise I'm being emotional when I'm making it because I have a glass heart and care about what happens to him, what he wants. (And even then it's scary because the withdrawal could hurt him just as easily.) It's the same thing as when I just can't put the dog out of his misery in Ostagar even though that could be considered a kindness in certain circumstances. But because I know I have an option to heal the dog, to give him a chance, I can't bring myself to kill him. There are a couple of perfectly pragmatic, rational decisions here and there that I just do not wish to make and when I feel that forcing myself would hurt my enjoyment of the game, I don't see a reason to push it. I want to experiment, but I also want to have fun and feel happy with my experience. Fortunately, there are plenty of other opportunities to make myself cry in these games.

Or just be a ruthless bastard without going too far out of my comfort zone.
But, anyway, I agree. I realise that different people would approach this decision completely differently. Just like in the examples you've given. The love interest vs truly pragmatic person. I don't see anything irrational about the latter. Nor do I think such a person must necessarily be heartless. I mean, how many templars do we meet? And they all (Or almost all.) look perfectly fine. I can even see how somebody could grow to believe taking lyrium is no big deal and make a decision out of ignorance. ("Cullen's just exaggerating," and the like.) I think this decision can be approached from quite a few angles.
I think your approach makes sense. With the characters you kill and all. And I make the same leap of faith with Zevran. I know it's absolutely irresponsible and naive to let him join when he just tried to kill you, but he's just too fun to shank right from the start.
Yeah, the corruption worries me, as well. I'm really torn on this one because, on one hand, I think Lavellan is not somebody who'd exactly happily jump at the first opportunity to work under the Chantry. On the other hand, the Inquisition, the way it is, has achieved much and the Divine is Lavellan's trusted friend and somebody who truly wishes to get **** done. I think your reasoning makes perfect sense, though. In fact, I like the idea of the organisation going ninja a lot, as well. I guess I'm still figuring out what my own character would even do.

My first playthroughs are always about exploring the game and my own character anyway. I tend to return to my favourite protags when I have a better understanding of everything. For all my talk about options, I still like to replay the same characters from time to time, adjusting their stories to what I think fits them best, etc.